Current Protein Identity：Q9UBQ0
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Difference tags compare only the current result set; every original PDB and assembly record remains separate.
Related-Structure Differences
Each row represents one biological assembly in one PDB entry; multiple monomers of the same protein are listed separately.
| PDB Entry | Assembly / Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Non-polymers | Experimental Method | Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|---|
| 1W24 Crystal Structure Of human Vps29 Deposited 2004-06-26 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
1–182（182 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
pH 7.5；25%PEG4000, 10%ETHYENE GLYCOL, 100MM HEPES PH7.5, pH 7.50
|
Resolution 2.10 Å R-free 0.244 |
| 2R17 Functional architecture of the retromer cargo-recognition complex Deposited 2007-08-22 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain A
1–182（182 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
hanging drop；pH 8；291 K；20% PEG 3350, 1M NaCl,50mM Tris, pH 8.0, hanging drop, temperature 291K
|
Resolution 2.80 Å R-free 0.268 |
| 2R17 Functional architecture of the retromer cargo-recognition complex Deposited 2007-08-22 | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain B
1–182（182 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | GOL GLYCEROL × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
hanging drop；pH 8；291 K；20% PEG 3350, 1M NaCl,50mM Tris, pH 8.0, hanging drop, temperature 291K
|
Resolution 2.80 Å R-free 0.268 |
| 5GTU Structural and mechanistic insights into regulation of the retromer coat by TBC1d5 Deposited 2016-08-23 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain A
2–182（181 aa）
Fragment：UNP residues 2-182
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
EVAPORATION；pH 6；289 K；0.1M Bis-Tris, pH6.0, 2% Tacsimate, pH 6.0, 15~20% PEG3350
|
Resolution 1.50 Å R-free 0.186 |
| 5OSH Structure of retromer VPS29-VPS35C subunits complexed with RidL N-terminal domain (1-236) Deposited 2017-08-17 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain A
1–182（182 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；0.1 M sodium chloride
0.1 M Tris pH 8.0
4-8% PEG6000.
|
Resolution 4.30 Å R-free 0.311 |
| 5OSH Structure of retromer VPS29-VPS35C subunits complexed with RidL N-terminal domain (1-236) Deposited 2017-08-17 | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain D
1–182（182 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；0.1 M sodium chloride
0.1 M Tris pH 8.0
4-8% PEG6000.
|
Resolution 4.30 Å R-free 0.311 |
| 5OSH Structure of retromer VPS29-VPS35C subunits complexed with RidL N-terminal domain (1-236) Deposited 2017-08-17 | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain G
1–182（182 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；0.1 M sodium chloride
0.1 M Tris pH 8.0
4-8% PEG6000.
|
Resolution 4.30 Å R-free 0.311 |
| 5OSH Structure of retromer VPS29-VPS35C subunits complexed with RidL N-terminal domain (1-236) Deposited 2017-08-17 | Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain J
1–182（182 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；0.1 M sodium chloride
0.1 M Tris pH 8.0
4-8% PEG6000.
|
Resolution 4.30 Å R-free 0.311 |
| 5OSI Structure of retromer VPS29-VPS35C subunits complexed with RidL harpin loop (163-176) Deposited 2017-08-17 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain A
1–182（182 aa）
|
Not recorded | EDO 1,2-ETHANEDIOL × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；0.1 M NaCl,
20% PEG3350
0.1 M Tris pH 8.5
|
Resolution 2.52 Å R-free 0.267 |
| 5OSI Structure of retromer VPS29-VPS35C subunits complexed with RidL harpin loop (163-176) Deposited 2017-08-17 | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain D
1–182（182 aa）
|
Not recorded | EDO 1,2-ETHANEDIOL × 2 NA SODIUM ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；0.1 M NaCl,
20% PEG3350
0.1 M Tris pH 8.5
|
Resolution 2.52 Å R-free 0.267 |
| 5OSI Structure of retromer VPS29-VPS35C subunits complexed with RidL harpin loop (163-176) Deposited 2017-08-17 | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain G
1–182（182 aa）
|
Not recorded | EDO 1,2-ETHANEDIOL × 2 NA SODIUM ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；0.1 M NaCl,
20% PEG3350
0.1 M Tris pH 8.5
|
Resolution 2.52 Å R-free 0.267 |
| 5OSI Structure of retromer VPS29-VPS35C subunits complexed with RidL harpin loop (163-176) Deposited 2017-08-17 | Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain J
1–182（182 aa）
|
Not recorded | EDO 1,2-ETHANEDIOL × 5 NA SODIUM ION × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；0.1 M NaCl,
20% PEG3350
0.1 M Tris pH 8.5
|
Resolution 2.52 Å R-free 0.267 |
| 5WYH Crystal structure of RidL(1-200) complexed with VPS29 Deposited 2017-01-13 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain A
2–182（181 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；0.1M Tris pH8.0, 20% PEG 8000
|
Resolution 2.46 Å R-free 0.225 |
| 5WYH Crystal structure of RidL(1-200) complexed with VPS29 Deposited 2017-01-13 | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain C
2–182（181 aa）
|
Not recorded | GOL GLYCEROL × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；0.1M Tris pH8.0, 20% PEG 8000
|
Resolution 2.46 Å R-free 0.225 |
| 6XS5 Crystal structure of human Vps29 complexed with RaPID-derived cyclic peptide RT-D1 Deposited 2020-07-15 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain A
1–182（182 aa）
|
Not recorded | GOL GLYCEROL × 2 FMT FORMIC ACID × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；3.5 M Sodium Formate
|
Resolution 2.01 Å R-free 0.225 |
| 6XS7 Crystal structure of human Vps29 complexed with RaPID-derived cyclic peptide RT-D2 Deposited 2020-07-15 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain A
1–182（182 aa）
|
Not recorded | GOL GLYCEROL × 2 FMT FORMIC ACID × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M Potassium thiocyanate, 30% PEG2000 MME
|
Resolution 1.58 Å R-free 0.191 |
| 6XS9 Crystal structure of human Vps29 complexed with RaPID-derived cyclic peptide RT-L1 Deposited 2020-07-15 | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
Chain A
1–182（182 aa）
|
Not recorded | MLI MALONATE ION × 2 GOL GLYCEROL × 3 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；1.4 M sodium malonate
|
Resolution 2.69 Å R-free 0.282 |
| 6XS9 Crystal structure of human Vps29 complexed with RaPID-derived cyclic peptide RT-L1 Deposited 2020-07-15 | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain B
1–182（182 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | GOL GLYCEROL × 1 O4B 1,4,7,10,13,16-HEXAOXACYCLOOCTADECANE × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；1.4 M sodium malonate
|
Resolution 2.69 Å R-free 0.282 |
| 6XSA Crystal structure of human Vps29 complexed with RaPID-derived cyclic peptide RT-L2 Deposited 2020-07-15 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain A
1–182（182 aa）
|
Not recorded | SO4 SULFATE ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；0.1 M HEPES, 1 M succinic and 1% PEG2000 MME
|
Resolution 1.83 Å R-free 0.227 |
| 7BLN VPS35/VPS29 arch of metazoan membrane-assembled retromer:SNX3 complex modelled with human proteins Deposited 2021-01-18 | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
Chain B
1–182（182 aa）
Chain D
1–182（182 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 8.90 Å |
| 8ESE Crystal structure of human Vps29 bound to a peptide from Vps35L Deposited 2022-10-13 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain Z
1–182（182 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；0.1 M Bis-tris pH 5.5 and 25% (w/v) PEG3350
|
Resolution 1.35 Å R-free 0.241 |
| 8P0V Structure of the human Commander complex coiled coils, DENND10 and partial Retriever subcomplex Deposited 2023-05-10 | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric（5） Consistent with protein count |
Chain N
1–182（182 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 6.50 Å |
| 8P0X Structure of the human Commander complex Retriever Subcomplex Deposited 2023-05-11 | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric（5） Consistent with protein count |
Chain N
1–182（182 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 7.50 Å |
| 8R02 Crystal structure of the retromer complex VPS29/VPS35 with the ligand bis-1,3-phenyl guanylhydrazone, 2a Deposited 2023-10-30 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain A
1–182（182 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.4；293 K；20% PEG 3350, 150 mM NaK tartrate, 100 mM NaCl, pH 7.4
|
Resolution 2.50 Å R-free 0.264 |
| 8R02 Crystal structure of the retromer complex VPS29/VPS35 with the ligand bis-1,3-phenyl guanylhydrazone, 2a Deposited 2023-10-30 | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain B
1–182（182 aa）
|
Not recorded | XFZ Bis-1,3-phenyl guanylhydrazon × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.4；293 K；20% PEG 3350, 150 mM NaK tartrate, 100 mM NaCl, pH 7.4
|
Resolution 2.50 Å R-free 0.264 |
| 8R0J Crystal structure of the retromer complex VPS29/VPS35 with the ligand bis-1,3-phenyl guanylhydrazone, 2a Deposited 2023-10-31 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain A
1–182（182 aa）
|
Not recorded | XFZ Bis-1,3-phenyl guanylhydrazon × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.4；293 K；18% PEG 3350, 150 mM NaK tartrate, pH 7.4;
|
Resolution 2.40 Å R-free 0.250 |
| 8R0J Crystal structure of the retromer complex VPS29/VPS35 with the ligand bis-1,3-phenyl guanylhydrazone, 2a Deposited 2023-10-31 | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain B
1–182（182 aa）
|
Not recorded | TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.4；293 K；18% PEG 3350, 150 mM NaK tartrate, pH 7.4;
|
Resolution 2.40 Å R-free 0.250 |
| 8RKS Structure of VPS29-VPS35 bound to the LFa motif R21 of Fam21. Deposited 2023-12-30 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain A
1–182（182 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；0.1 M NaCl, 20% PEG3350 0.1 M Tris pH 8.5
|
Resolution 3.10 Å R-free 0.288 |
| 8RKS Structure of VPS29-VPS35 bound to the LFa motif R21 of Fam21. Deposited 2023-12-30 | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain C
1–182（182 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；0.1 M NaCl, 20% PEG3350 0.1 M Tris pH 8.5
|
Resolution 3.10 Å R-free 0.288 |
| 8RKS Structure of VPS29-VPS35 bound to the LFa motif R21 of Fam21. Deposited 2023-12-30 | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain E
1–182（182 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；0.1 M NaCl, 20% PEG3350 0.1 M Tris pH 8.5
|
Resolution 3.10 Å R-free 0.288 |
| 8RKS Structure of VPS29-VPS35 bound to the LFa motif R21 of Fam21. Deposited 2023-12-30 | Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain G
1–182（182 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；0.1 M NaCl, 20% PEG3350 0.1 M Tris pH 8.5
|
Resolution 3.10 Å R-free 0.288 |
| 8SYM Human VPS29/VPS35L Complex (Locally refined map) Deposited 2023-05-25 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain B
1–186（186 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7；10 mM HEPES (pH 7.0), 150 mM NaCl, 2 mM MgCl2, 2 mM DTT, and 5% (v/v) glycerol
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 8SYN Human VPS35L/VPS29/VPS26C Complex Deposited 2023-05-25 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain B
1–186（186 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7；10 mM HEPES (pH 7.0), 150 mM NaCl, 2 mM MgCl2, 2 mM DTT, and 5% (v/v) glycerol
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.94 Å |
| 8SYO Human Retriever VPS35L/VPS29/VPS26C Complex (Composite Map) Deposited 2023-05-25 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain B
1–186（186 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7；10 mM HEPES (pH 7.0), 150 mM NaCl, 2 mM MgCl2, 2 mM DTT, and 5% (v/v) glycerol
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.94 Å |
| 9AU7 Human Retriever VPS35L/VPS29/VPS26C complex bound to SNX17 peptide (Composite Map) Deposited 2024-02-28 | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
Chain B
1–186（186 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |